Are you trying to use more than 1 flow cell and split your samples across different flow cells with different runs? You should try to avoid batching if you can to not deal with potential batch affects. You need to think about what those reads will do, are they for counting or genotyping. If you are counting, do you really need 1000 coverage per fragment, would 100x per fragment be OK for statistical purposes? Generally the more samples you multiplex the less reads/coverage per sample and vice versa. The NGS library kit should have some guidelines in the handbook for how many samples to multiplex given the size of the panel for a given panel size and coverage. Think of this, if you put 24 sample and got 30,000,000 reads per sample on average, then if you put twice as many samples it will roughly be 15 million reads per samples if you get similar cluster pass filter and total output as the run with 24 samples and 30 million reads (not every run has the same total Gb output). I would highly recommend you contact a field application scientist or someone who has used to kit to engage you on this topic if the above mentioned guidelines aren't in the kit handbook.